Quantitative trait locus (QTL) mapping is an efficient approach to discover the genetic architecture underlying complex quantitative traits. However, the low density of molecular markers in genetic maps has limited the efficiency and accuracy of QTL mapping. In this study, specific length amplified fragment sequencing (SLAF-seq), a new high-throughput strategy for large-scale SNP discovery and genotyping based on next generation sequencing (NGS), was employed to construct a high-density soybean genetic map using recombinant inbred lines (RILs, Luheidou2 x Nanhuizao, F5:8). With this map, the consistent QTLs for isoflavone content across various environments were identified.

Soybean (Glycine max L. Merrill) isoflavones are secondary metabolites of great interest because of their beneficial impact on human health. We profiled the seed isoflavone composition of 1168 soybean accessions collected from diverse ecoregions of China in three locations over two years. We observed significant differences in isoflavone content among the accessions, accession types, years of growth and ecoregions of origin. Total isoflavone (TIF) concentration of the soybean accessions ranged from 745 μg g-1 to 5253.98 μg g-1, which represents a 7-fold difference. The highest mean TIF concentration (2689.27 μg g-1) was observed in the Huang Huai Hai Valley Region (HR) accessions, followed by accessions from the Southern Region (SR) and Northern Region (NR) with TIF concentration of 2518.91 μg g-1 and 1942.78 μg g-1, respectively. Thirty-five accessions were identified as elite soybean resources based on their higher TIF concentration (4024.74 μg g-1 to 5253.98 μg g-1). Pairwise correlation analysis showed significant positive correlations between individual isoflavones and TIF concentrations. Malonyldaidzin and malonylgenistin showed the highest correlations with TIF concentration (r = 0.90 and r = 0.92, respectively), whereas acetyldaidzin showed the lowest correlation. The main isoflavone components had significant negative correlations with latitude and longitude, indicating that the geographical origin of the accessions influenced their seed isoflavone composition. Based on principal component analysis, glycosides and malonylglycosides of isoflavones were the major discriminative components for the soybean accessions. The present study demonstrated the geographical distribution of soybean seed isoflavone concentrations across the main ecoregion of China. The identified soybean accessions with both high and low TIF concentrations, which are desirable materials for industrial uses and could also be used as parents to breed soybean lines with improved isoflavone quantity and composition in the seeds.

Soybean (Glycine max L. Merr.) is one of the most important crops in the world. Its major content of vegetable oil made it widely used for human consumption and several food industries. To investigate the variation in seed fatty acid composition of soybeans from different origins, a set of 633 soybean accessions originated from four diverse germplasm collections—including China, United States of America (USA), Japan, and Russia—were grown in three locations, Beijing, Anhui, and Hainan for two years. The results showed significant differences (P < 0.001) among the four germplasm origins for all fatty acid contents investigated. Higher levels, on average, of palmitic acid (PA) and linolenic acid (LNA) were observed in Russian germplasm (12.31% and 8.15%, respectively), whereas higher levels of stearic acid (SA) and oleic acid (OA) were observed in Chinese germplasm (3.95% and 21.95%, respectively). The highest level of linoleic acid (LA) was noticed in the USA germplasm accessions (56.34%). The largest variation in fatty acid composition was found in LNA, while a large variation was observed between Chinese and USA germplasms for LA level. Maturity group (MG) significantly (P < 0.0001) affected all fatty acids and higher levels of PA, SA, and OA were observed in early maturing accessions, while higher levels of LA and LNA were observed in late maturing accessions. The trends of fatty acids concentrations with different MG in this study further provide an evidence of the importance of MG in breeding for such soybean seed components. Collectively, the unique accessions identified in this study can be used to strengthen the soybean breeding programs for meeting various human nutrition patterns around the globe.

In order to ensure an ongoing and long-term breeding progress of soybean, stable sources of major quality traits across multi-environments need to be identified. Here, a panel of 135 soybean genotypes was tested in three different Chinese environments, including Beijing, Anhui, and Hainan during the 2017 and 2018 growing seasons to identify stable genotypes for cultivation under varying environmental conditions. The weighted average of absolute scores biplot (WAASB) for the best linear unbiased predictions of the genotype-environment interaction and multi-trait stability index (MTSI) were utilized to determine the stability of the soybeans for seven seed composition traits viz; protein content, oil content, and five fatty acids (palmitic, stearic, oleic, linoleic, and linolenic acids). Based on the WAASB index, the following genotypes were identified as stable genotypes for some specific traits; ZDD12828 and ZDD12832 for protein content, WDD01583 and WDD03025 for oil content, ZDD23040 for palmitic acid, WDD00033 for stearic acid, ZDD23822 for oleic acid, ZDD11183 for linoleic acid, and ZDD08489 for linolenic acid. Furthermore, based on MTSI at a selection intensity of 10%, 14 soybean genotypes were selected for their average performance and stability. Overall, the MTSI was shown to be a powerful and simple tool for identifying superior genotypes in terms of both performance and stability, hence, identifying stable soybean genotypes for future breeding programs of quality traits.